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Hi. I'm adding my "two cents" here at James' request, but I'm not sure I can be very helpful in pinning anything down.
I too have seen here the error noted in this thread's title. It has caused me to lose my "inputs" often enough, in fact, that I'm now more careful than ever to prepare and save messages and replies off line prior to any posting attempt. However, I would also have to say that any relationship to other issues, such as those involved in our Netquery development work, is tenouous and unproven.
In developing the Netquery module, we ran into several problems that appear to have been involved simultaneously and, at the time, I was much more concerned about eliminating the difficulties than I was about causal relationships. Thus it is difficult to attribute specific aspects of those problems to a particular cause. The best I can do is to list some factors:
1) The XOOPS module installer appears to have some difficulties with handling some phpMyAdmin exports, especially large ones. Version specificity may be involved as with, for example, the recent change in phpMyAdmin's comment character.
2) It appears that some hosting service providers (my 1and1.com "business package" host for sure) are imposing their own "unadvertised" restrictions on SQL queries. Even their senior support staff may be unaware of these restrictions which, in the case I now know about, limited data inserts to about 2000 records each.
3) Host configuration settings for both PHP and MySQL can also be involved and may or may not be capable of being overridden by individual accounts with either .htaccess or php.ini local settings. PHP script timeout is mentioned briefly in "carnuke's" excellent FAQ, but there are others as well that can be significant for data handling ops.
That's about as much as I can say with any certainty about the situations I have encountered myself. Hope it helps to at least open some routes for further exploration.